biotite.sequence.graphics.LetterTypePlotter¶
- class biotite.sequence.graphics.LetterTypePlotter(axes, alphabet, color_scheme=None, color_symbols=False, font_size=None, font_param=None)[source]¶
Bases:
LetterPlotterThis SymbolPloter colors each symbol based on the general color of that symbol defined by a color scheme.
EXPERIMENTAL: Future API changes are probable.
- Parameters
- axesAxes
A Matplotlib axes, that is used as plotting area.
- alphabetAlphabet
The alphabet of the alignment(s) to be plotted
- color_schemestr or list of (tuple or str), optional
Either a valid color scheme name (e.g.
"rainbow","clustalx",blossom, etc.) or a list of Matplotlib compatible colors. The list length must be at least as long as the length of the alphabet used by the sequences.- color_symbolsbool, optional
If true, the symbols themselves are colored. If false, the symbols are black, and the boxes behind the symbols are colored.
- font_sizefloat, optional
Font size of the sequence symbols.
- font_paramdict, optional
Additional parameters that is given to the
matplotlib.Textinstance of each symbol.
- get_color(alignment, column_i, seq_i)¶
Get the color of a symbol at a specified position in the alignment.
The symbol is specified as position in the alignment’s trace (
trace[pos_i, seq_i]).PROTECTED: Override when inheriting.
- Parameters
- alignmentAlignment
The respective alignment.
- column_iint
The position index in the trace.
- seq_iint
The sequence index in the trace.
- Returns
- colorobject
A Matplotlib compatible color used for the background or the symbol itself at the specifed position
- plot_symbol(bbox, alignment, column_i, seq_i)¶
Get the color of a symbol at a specified position in the alignment.
The symbol is specified as position in the alignment’s trace (
trace[pos_i, seq_i]).- Parameters
- bboxBbox
The axes area to plot the symbol in
- alignmentAlignment
The respective alignment.
- column_iint
The position index in the trace.
- seq_iint
The sequence index in the trace.
